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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PCDHAC1 Gene

protein-coding   GIFtS: 37
GCID: GC05P140424

protocadherin alpha subfamily C, 1

 Explore 1 disease affiliated with
PCDHAC1 via our new
 Human Malady Compendium 
Biological research products
for PCDHAC1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Protocadherin Alpha Subfamily C, 11 2
PCDH-ALPHA-C12
Protocadherin Alpha-C12
PCDH-Alpha-C11

External Ids:    HGNC: 86761   Entrez Gene: 561352   Ensembl: ENSG000002483837   OMIM: 6063205   UniProtKB: Q9H1583   

Export aliases for PCDHAC1 gene to outside databases

Previous GC identifers: GC05U990126 GC05P140149 GC05P140214 GC05P140221 GC05P140176 GC05P140178 GC05P140286 GC05P140252 GC05P140261 GC05P140271 GC05P140280 GC05P140291 GC05P140301 GC05P140310 GC05P140313 GC05P140320 GC05P140343 GC05P135451 GC05P140354 GC05P140375 GC05P140394 GC05P140408


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PCDHAC1:
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on
chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene
clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and
consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons,
or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in
the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons
encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins
that most likely play a critical role in the establishment and function of specific cell-cell connections in the
brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature
has yet to be determined. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of
specific neuronal connections in the brain




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDHAC1 gene promoter:
         GR   SRF   AML1a   SRF (504 AA)   GATA-1   HOXA5   SEF-1 (1)   Msx-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHAC1 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHAC1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHAC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHAC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHAC1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140424:  view genomic region     (about GC identifiers)

Start:
140,306,302 bp from pter      End:
140,391,929 bp from pter
Size:
85,628 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158 (See protein sequence)
Recommended Name: Protocadherin alpha-C1 precursor  
Size: 963 amino acids; 103942 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: Q9Y5F5 Q9Y5I5
Alternative splicing: 2 isoforms:  Q9H158-1   Q9H158-2   

Explore the universe of human proteins at neXtProt for PCDHAC1: NX_Q9H158

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H158

  • PCDHAC1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_061721.2  NP_114088.2  

    ENSEMBL proteins: 
     ENSP00000253807   ENSP00000386356  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral to plasma membrane TAS10380929


    PCDHAC1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    PCDHAC1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q9H158

    ProtoNet protein and cluster: Q9H158

    1 Blocks protein family: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158
    Similarity: Contains 6 cadherin domains


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of
    specific neuronal connections in the brain

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    hsa-miR-194* hsa-miR-3130-5p hsa-miR-4272 hsa-miR-106a hsa-miR-15a hsa-miR-485-3p hsa-miR-4305 hsa-miR-3653
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--


    PCDHAC1 for ontologies           About GeneDecksing


    Animal Models:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Pcdhac1):
     normal 

    PCDHAC1 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDHAC1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for PCDHAC1 (ENSP000002538074) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RELNENSP000003924234STRING: ENSP00000392423
    CRKENSP000003005744STRING: ENSP00000300574
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion TAS10380929
    GO:0007156homophilic cell adhesion IEA--
    GO:0007399nervous system development TAS10380929


    PCDHAC1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PCDHAC1

    1 HMDB Compound for PCDHAC1    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about PCDHAC1 / PCDC1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PCDHAC1 gene (2 alternative transcripts): 
    NM_018898.3  NM_031882.2  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000253807(uc003lih.2) ENST00000409700(uc003lig.1)

    miRNA
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    8/115 QIAGEN miScript miRNA Assays for microRNAs that regulate PCDHAC1 (see all 115):
    hsa-miR-194* hsa-miR-3130-5p hsa-miR-4272 hsa-miR-106a hsa-miR-15a hsa-miR-485-3p hsa-miR-4305 hsa-miR-3653
    SwitchGear 3'UTR luciferase reporter plasmidPCDHAC1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PCDHAC1 (see all 7)
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    24/261 AceView cDNA sequences (see all 261):

    AF152476 NM_031497 AW152471 NM_018899 AF152483 NM_031849 BF933281 NM_031882 
    BM129562 NM_018907 NM_018911 NM_018903 CA488079 NM_031860 AF152484 NM_031861 
    BM970705 NM_018906 AF152304 NM_031411 AA384862 AF152477 AF152312 NM_031496 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PCDHAC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See PCDHAC1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHAC1
        SABiosciences Custom PCR Arrays for PCDHAC1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHAC1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHAC1 gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    --
    (see all 5)
    Uncharacterized protein
    (see all 5)
    40(a)
    40(a)
    (see all 5)
    possible ortholog
    possible ortholog
    (see all 5)
    Un(45427780-45446576)
    13(562057-583011)
    lizard
    (Anolis carolinensis)
    Reptilia D0IQ25_ANOCA6
    --
    (see all 16)
    --
    50(a)
    41(a)
    (see all 16)
    1 ↔ 1
    possible ortholog
    (see all 16)
    4(77250923-77253391)
    AAWZ02039895(5757-7706)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh2g76
    pcdh2g66
    (see all 44)
    protocadherin 2 gamma 6
    (see all 44)
    40(a)
    40(a)
    (see all 44)
    many ↔ many
    many ↔ many
    (see all 44)
    14(2882604-2884979)
    14(2878900-2881275)


    ENSEMBL Gene Tree for PCDHAC1 (if available)
    TreeFam Gene Tree for PCDHAC1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHAC1 gene
    PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  PCDHGB22  
    PCDHGA82  PCDHGA92  PCDHGB32  PCDHGC32  PCDHGB62  PCDHA62  PCDHGA52  PCDHA82  
    PCDHA132  PCDHB52  PCDHB132  PCDHA32  PCDHGA42  PCDHGA72  PCDHA42  PCDHB42  
    PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  PCDHA122  PCDHB82  PCDHA52  
    PCDHGB12  PCDHGB42  PCDHA12  PCDHGA22  PCDHA112  PCDHA72  PCDHGA112  PCDHGA62  
    PCDHB32  PCDHB62  PCDHGC52  PCDHGC42  PCDHA102  PCDHA92  PCDHGA12  PCDHB102  
    PCDHB12  PCDHGA32  PCDHGB72  
    18/64 SIMAP similar genes for PCDHAC1 using alignment to 2 protein entries:     PCDC1_HUMAN (see all proteins) (see all similar genes):
    PCDHGA3    PCDHAC2    DKFZp586I1919    PCDHB18    PCDHGA11    PCDHA3
    PCDHA6    PCDHA8    PCDHB15    PCDHGA1    PCDHGB1    PCDH10
    PCDHA1    PCDHA10    PCDHA2    PCDHA4    PCDHA7    PCDHB12

    PCDHAC1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for PCDHAC1
         2 CNVs: 99310 3578
    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHAC1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    PCDHAC1 for disorders           About GeneDecksing

    OMIM gene information: 606320    OMIM disorders: --

    1 disease for PCDHAC1:    About MalaCards
    neuronitis


    Export disorders for PCDHAC1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PCDHAC1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PCDHAC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (1999)
    2. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PubMed id 22589738)1 Fox C.S....Borecki I.B. (2012)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    5. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (2000)
    6. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1 Sugino H....Yagi T. (2000)
    7. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
    8. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 56135 HGNC: 8676 AceView: PCDHA9 Ensembl:ENSG00000248383 euGenes: HUgn56135
    ECgene: PCDHAC1 H-InvDB: PCDHAC1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PCDHAC1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PCDHAC1 gene:
    Search GeneIP for patents involving PCDHAC1

    GeneCards and IP:
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